The purpose of the Protein Chemistry and Proteomics Shared Resource is to provide essential services in peptide synthesis, protein separation, electrophoresis, protein identification, mass spectrometry, differential proteomics, biomarker discovery, small molecule analysis and peptide quantification, computing informatics and in silico molecular modeling to Cancer Center members. This is accomplished by providing state-of-theart services, expertise and technologies. Services include: (1) Solid phase peptide synthesis by Fmoc orthogonal chemistry; (2) Synthesis of peptide/protein specific immunogens; (3) Protein separation by reverse phase HPLC and FPLC methods; (4) one-dimensional (1-D) and 2-dimensional (2-D) PAGE of protein mixtures including DIGE separation and analysis; (5) Edman chemical sequencing; (6) Protein identification by nanoLC-MS/MS methods; (7) Differential Proteomics / Biomarker discovery by tandem MS and targeted MS (e.g., MRM) methods; (8) Small molecule analysis by LC-MS and MRM methods; (9) Protein PTM analysis by nanoLC-FT-ICR mass spectrometry, and (10) Computational services for peptide design, de novo modeling of proteins, protein identification, and differential proteomics using iTRAQ and label-free methods. Future plans of the shared resource will include the development of Electron Transfer Dissociation (ETD) mass spectrometry for efficient mapping of protein post-translational modifications and chemical peptide ligation synthesis utilizing thioester methods for the chemical synthesis of small proteins and polypeptides. Cancer Center member use of the Shared Resource has increased by nearly 38% over this grant period, to more than 97 members in 2007. Cancer Center use represents 65% of the total services provided by the Shared Resource. The Protein Chemistry and Proteomics Shared Resource has been vital to Cancer Center members supporting a broad array of peer review funded research that has produced more than 400 publications during the current funding period.